The Department of Environmental Protection (DEP) had to stop construction on the Flushing Tunnel and had to change some details in the reconstruction of the Gowanus Pumping Station due to Hurricane Sandy.

The goal of the two projects was to improve wastewater treatment infrastructure, however the storm caused the pumping station to malfunction.

According to DEP, 10 of 14 wastewater treatment facilities had some damage. Of the 96 pumping stations, 42 were damaged, however at this point all are back online and working. The total cost of the damages sustained by DEP is estimated at $96 million.

“We’re actively coordinating with FEMA to get some of that money reimbursed,” Jill Stein, director of wet weather planning and water quality policy for DEP, told members of Community Board 6 Monday night.

One of the heavily affected areas was the Gowanus Canal pumping station, which sustained damages and needed a backup generator, which took time to kick in.

“The pumping station was offline for approximately 33 hours,” Stein said.

This caused 13 million gallons of raw sewage to discharge into the canal. She said that as soon as the pumping station was back online and running, the bypass was halted.

The oxygen transfer system was also damaged at the pumping station, and is not currently functional. Stein said that it is likely that it will be restored by Memorial Day.

Stein said that while the water quality was affected due to the discharge, the water was back to normal conditions since roughly November. She said DEP is testing the water regularly.

Although the pumping station was damaged, the construction of the project is still underway. Stein said that 61 percent of the project is complete and that most of it will be completed by the end of this year.

DEP will now add a design element to the pumping station to prevent storm surge from affecting the facility in the future.

Overall, DEP has roughly $225 million invested in the Gowanus Canal, which is mostly allotted for the pumping station and the tunnel.

The Flushing Tunnel project will be delayed until June due to a leak and a Con Edison work stoppage. DEP was ahead of schedule on both projects, so it is still planning on meeting the deadline of September 2014 for completion.

In a piece of irony, Sandy – which many see as a result of climate change – forced DEP to halt a two-year study on climate change and its impact on wastewater treatment facilities and infrastructure.

However, DEP used the hurricane to get a better understanding of what they need to do if storms like Sandy become more common. Stein said that the agency is now looking into every major facility to determine what needs to be done to prevent future damage.

“The idea is to do this critical vulnerability assessment and identify and evaluate adaptation strategies,” she said.